[English] 日本語
Yorodumi
- PDB-4oqu: Structure of the SAM-I/IV riboswitch (env87(deltaU92)) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oqu
TitleStructure of the SAM-I/IV riboswitch (env87(deltaU92))
ComponentsSAM-I/IV riboswitch
KeywordsRNA / riboswitch / aptamer / pseudoknot / regulation / S-adenosylmethionine
Function / homologyS-ADENOSYLMETHIONINE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTrausch, J.J. / Reyes, F.E. / Edwards, A.L. / Batey, R.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for diversity in the SAM clan of riboswitches.
Authors: Trausch, J.J. / Xu, Z. / Edwards, A.L. / Reyes, F.E. / Ross, P.E. / Knight, R. / Batey, R.T.
History
DepositionFeb 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SAM-I/IV riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1427
Polymers31,6221
Non-polymers5206
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.269, 127.269, 181.609
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

-
Components

#1: RNA chain SAM-I/IV riboswitch


Mass: 31622.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 transcription
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal growTemperature: 303.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1:1 mix of RNA mix and mother liquor. RNA mix contained RNA and 1 mM SAM. Mother liquor contained 50 mM Na-cacodylate, pH 7.0, 250 mM ammonium acetate, 20 mM MgCl2, and 16% 2-methyl-2,4- ...Details: 1:1 mix of RNA mix and mother liquor. RNA mix contained RNA and 1 mM SAM. Mother liquor contained 50 mM Na-cacodylate, pH 7.0, 250 mM ammonium acetate, 20 mM MgCl2, and 16% 2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 303.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 17, 2014
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.2→41.66 Å / Num. all: 14952 / Num. obs: 14916 / % possible obs: 99.8 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9
Reflection shellResolution: 3.2→3.31 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→31.408 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 1486 10 %10%
Rwork0.1957 ---
obs0.1987 14854 99.42 %-
all-14854 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→31.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2100 32 0 2132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062383
X-RAY DIFFRACTIONf_angle_d1.2523718
X-RAY DIFFRACTIONf_dihedral_angle_d12.8841162
X-RAY DIFFRACTIONf_chiral_restr0.052491
X-RAY DIFFRACTIONf_plane_restr0.00799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.30320.39821320.35471183X-RAY DIFFRACTION100
3.3032-3.42110.32271290.31781186X-RAY DIFFRACTION99
3.4211-3.55790.30011330.29631194X-RAY DIFFRACTION99
3.5579-3.71960.28441320.24641175X-RAY DIFFRACTION99
3.7196-3.91540.27291330.22781198X-RAY DIFFRACTION100
3.9154-4.16020.22421330.2141195X-RAY DIFFRACTION100
4.1602-4.48050.23181350.19831210X-RAY DIFFRACTION100
4.4805-4.92990.24611350.16461225X-RAY DIFFRACTION100
4.9299-5.63970.1731370.14851223X-RAY DIFFRACTION100
5.6397-7.09190.18881400.16541260X-RAY DIFFRACTION100
7.0919-31.40930.20891470.1821319X-RAY DIFFRACTION98

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more